def test_calc_lfp_pointsource_moi_doubling(self):
"""
Test that slice with zero-conductivity MEA region (z<0) has twice
the potential as in vivo case at MEA electrode plane
"""
sigma_T = 0.3
sigma_G = 0.0
sigma_S = 0.3
h = 200
steps = 3
cell = TestCell()
cell.zstart[0] = 50
cell.zmid[0] = 50
cell.zend[0] = 50
in_vivo = lfpcalc.calc_lfp_pointsource(cell,
x=50., y=0, z=0, sigma=sigma_T,
r_limit=cell.diam/2)
in_vitro = lfpcalc.calc_lfp_pointsource_moi(cell,
x=50, y=0, z=0, sigma_T=sigma_T,
sigma_G=sigma_G, sigma_S=sigma_S,
r_limit=cell.diam/2, h=h, steps=steps)
np.testing.assert_almost_equal(2 * in_vivo, in_vitro, decimal=9)
def test_calc_lfp_pointsource_moi_doubling(self):
"""
Test that slice with zero-conductivity MEA region (z<0) has twice
the potential as in vivo case at MEA electrode plane
"""
sigma_T = 0.3
sigma_G = 0.0
sigma_S = 0.3
h = 200
steps = 3
cell = DummyCell()
cell.zstart[0] = 50
cell.zmid[0] = 50
cell.zend[0] = 50
in_vivo = lfpcalc.calc_lfp_pointsource(cell,
x=50., y=0, z=0, sigma=sigma_T,
r_limit=cell.diam/2)
in_vitro = lfpcalc.calc_lfp_pointsource_moi(cell,
x=50, y=0, z=0, sigma_T=sigma_T,
sigma_G=sigma_G, sigma_S=sigma_S,
r_limit=cell.diam/2, h=h, steps=steps)
np.testing.assert_almost_equal(2 * in_vivo, in_vitro, decimal=9)
def test_lfpcalc_calc_lfp_pointsource_moi_00(self):
"""
Test slice where all layers have same conductivity reproduces
isotropic case.
"""
sigma_T = 0.3
sigma_G = 0.3
sigma_S = 0.3
h = 300
steps = 20
cell = DummyCell(np.array([[h / 2, h / 2]]))
in_vivo = lfpcalc.calc_lfp_pointsource(cell,
x=0.5,
y=0,
z=1,
sigma=sigma_T,
r_limit=cell.d / 2)
in_vitro = lfpcalc.calc_lfp_pointsource_moi(cell,
x=0.5,
y=0,
z=1,
sigma_T=sigma_T,
sigma_G=sigma_G,
sigma_S=sigma_S,
r_limit=cell.d / 2,
h=h,
steps=steps)
np.testing.assert_equal(in_vivo, in_vitro)
def test_lfpcalc_calc_lfp_pointsource_moi_02(self):
"""
Very close to point source, in vivo and in vitro have similar results,
e.g., the positions should be adjusted similarly.
"""
sigma_T = 0.3
sigma_G = 0.0
sigma_S = 1.5
h = 2000
steps = 20
cell = DummyCell(z=np.array([[h / 2, h / 2]]))
in_vivo = lfpcalc.calc_lfp_pointsource(cell,
x=0.5,
y=0,
z=h / 2,
sigma=sigma_T,
r_limit=cell.d / 2)
in_vitro = lfpcalc.calc_lfp_pointsource_moi(cell,
x=0.5,
y=0,
z=h / 2,
sigma_T=sigma_T,
sigma_G=sigma_G,
sigma_S=sigma_S,
r_limit=cell.d / 2,
h=h,
steps=steps)
np.testing.assert_almost_equal(in_vivo, in_vitro, 4)
def test_calc_lfp_pointsource_moi_too_close(self):
"""
Very close to point source, in vivo and in vitro have similar results,
e.g., the positions should be adjusted similarly.
"""
sigma_T = 0.3
sigma_G = 0.0
sigma_S = 1.5
h = 2000
steps = 20
cell = TestCell()
cell.zmid[0] = h / 2
cell.zstart[0] = h / 2
cell.zend[0] = h / 2
in_vivo = lfpcalc.calc_lfp_pointsource(cell,
x=0.5,
y=0,
z=h / 2,
sigma=sigma_T,
r_limit=cell.diam / 2)
in_vitro = lfpcalc.calc_lfp_pointsource_moi(cell,
x=0.5,
y=0,
z=h / 2,
sigma_T=sigma_T,
sigma_G=sigma_G,
sigma_S=sigma_S,
r_limit=cell.diam / 2,
h=h,
steps=steps)
np.testing.assert_almost_equal(in_vivo, in_vitro, 4)
def test_calc_lfp_pointsource_moi_homogeneous(self):
"""
Test that slice where all layers have same conductivity reproduces
in vivo results.
"""
sigma_T = 0.3
sigma_G = 0.3
sigma_S = 0.3
h = 300
steps = 20
cell = TestCell()
cell.zmid[0] = h / 2
cell.zstart[0] = h / 2
cell.zend[0] = h / 2
in_vivo = lfpcalc.calc_lfp_pointsource(cell,
x=0.5,
y=0,
z=1,
sigma=sigma_T,
r_limit=cell.diam / 2)
in_vitro = lfpcalc.calc_lfp_pointsource_moi(cell,
x=0.5,
y=0,
z=1,
sigma_T=sigma_T,
sigma_G=sigma_G,
sigma_S=sigma_S,
r_limit=cell.diam / 2,
h=h,
steps=steps)
np.testing.assert_equal(in_vivo, in_vitro)
def test_calc_lfp_pointsource(self):
"""Test that function calc_lfp_pointsource
reproduces analytic formula"""
sigma = 0.3
cell = TestCell()
np.testing.assert_equal(1./(4*np.pi*sigma),
lfpcalc.calc_lfp_pointsource(cell,
x=0.5, y=0, z=1, sigma=sigma,
r_limit=cell.diam/2))
def test_calc_lfp_pointsource(self):
"""Test that function calc_lfp_pointsource
reproduces analytic formula"""
sigma = 0.3
cell = DummyCell()
np.testing.assert_equal(1./(4*np.pi*sigma),
lfpcalc.calc_lfp_pointsource(cell,
x=0.5, y=0, z=1, sigma=sigma,
r_limit=cell.diam/2))
def test_calc_lfp_pointsource_moi_homogeneous(self):
"""
Test that slice where all layers have same conductivity reproduces
in vivo results.
"""
sigma_T = 0.3
sigma_G = 0.3
sigma_S = 0.3
h = 300
steps = 20
cell = TestCell()
cell.zmid[0] = h/2
cell.zstart[0] = h/2
cell.zend[0] = h/2
in_vivo = lfpcalc.calc_lfp_pointsource(cell,
x=0.5, y=0, z=1, sigma=sigma_T,
r_limit=cell.diam/2)
in_vitro = lfpcalc.calc_lfp_pointsource_moi(cell,
x=0.5, y=0, z=1, sigma_T=sigma_T,
sigma_G=sigma_G, sigma_S=sigma_S,
r_limit=cell.diam/2, h=h, steps=steps)
np.testing.assert_equal(in_vivo, in_vitro)
def test_calc_lfp_pointsource_moi_too_close(self):
"""
Very close to point source, in vivo and in vitro have similar results,
e.g., the positions should be adjusted similarly.
"""
sigma_T = 0.3
sigma_G = 0.0
sigma_S = 1.5
h = 2000
steps = 20
cell = TestCell()
cell.zmid[0] = h/2
cell.zstart[0] = h/2
cell.zend[0] = h/2
in_vivo = lfpcalc.calc_lfp_pointsource(cell,
x=0.5, y=0, z=h/2, sigma=sigma_T,
r_limit=cell.diam/2)
in_vitro = lfpcalc.calc_lfp_pointsource_moi(cell,
x=0.5, y=0, z=h/2, sigma_T=sigma_T,
sigma_G=sigma_G, sigma_S=sigma_S,
r_limit=cell.diam/2, h=h, steps=steps)
np.testing.assert_almost_equal(in_vivo, in_vitro, 4)
